read.rg {CALIB} | R Documentation

## Read RGList_CALIB from Image Analysis Output Files

### Description

Reads an RGList_CALIB from a series of microarray image analysis output files

### Usage

    read.rg(files = NULL, source = "generic", path = NULL, ext = NULL,
            names = NULL, columns = NULL, other.columns = NULL,
            annotation = NULL,wt.fun = NULL, verbose = TRUE, sep = "\t",
            quote = NULL, DEBUG = FALSE, ...)

### Arguments

`files` | character vector giving the names of the files containing image analysis output or, for Imagene data, a character matrix of names of files. If omitted, then all files with extension `ext` in the specified directory will be read in alphabetical order.
`source` | character string specifying the image analysis program which produced the output files. Choices are `"generic"`, `"agilent"`, `"arrayvision"`, `"bluefuse"`, `"genepix"`, `"genepix.custom"`, `"genepix.median"`, `"imagene"`, `"quantarray"`, `"scanarrayexpress"`, `"smd.old"`, `"smd"`, `"spot"` or `"spot.close.open"`.
`path` | character string giving the directory containing the files. The default is the current working directory.
`ext` | character string giving optional extension to be added to each file name
`names` | character vector of names to be associated with each array as column name. Defaults to `removeExt(files)`.
`columns` | list with fields `R`, `G`, `Rb`, `Gb`, `RArea` and `GArea` giving the column names to be used for red foreground, green foreground, red background, green background, red area and green area respectively. Or, in the case of Imagene data, a list with fields `f` and `b`. This argument is optional if `source` is specified, otherwise it is required.
`other.columns` | character vector of names of other columns to be read containing spot-specific information
`annotation` | character vector of names of columns containing annotation information about the probes
`wt.fun` | function to calculate spot quality weights
`verbose` | logical, `TRUE` to report each time a file is read
`sep` | the field separator character
`quote` | character string of characters to be treated as quote marks
`DEBUG` | a logical value, if `TRUE`, a series of echo statements will be printed for each file. Details on the file, skip, and selected columns in a colClasses format for read.table will be displayed.
`...` | any other arguments are passed to `read.table`.

### Details

This is the main data input function for CALIB package. It has the similar usage as the read.maimages function in limma package. The output of the function is an `RGList_CALIB` object. However,there are two more fields - `$RArea` and `$GArea` than `RGList` object in limma package. These two fields contain spot area of each color. More details see `read.maimages` in limma package.

### Value

An `RGList_CALIB` object containing the components

`R` | matrix containing the red channel foreground intensities for each spot for each array.
`G` | matrix containing the green channel foreground intensities for each spot for each array.
`Rb` | matrix containing the red channel background intensities for each spot for each array.
`Gb` | matrix containing the green channel background intensities for each spot for each array.
`RArea` | matrix containing the red spot area for each spot for each array.
`GArea` | matrix containing the green spot area for each spot for each array.
`weights` | spot quality weights, if `wt.fun` is given
`other` | list containing matrices corresponding to `other.columns` if given
`genes` | data frame containing annotation information about the probes, for example gene names and IDs and spatial positions on the array, currently set only if `source` is `"agilent"`, `"genepix"` or `source="imagene"` or if the `annotation` argument is set
`targets` | data frame with column `FileName` giving the names of the files read
`source` | character string giving the image analysis program name
`printer` | list of class `PrintLayout`, currently set only if `source="imagene"`

### Author(s)

Hui Zhao

### References

`read.maimages` in limma package

### See Also

'read.rg' is based on `read.table` in the base package

### Examples

     #  Read all .gpr files from current working directory.

     # files <- dir(pattern="*\.gpr$")
     # RG <- read.rg(files,"genepix")

[Package CALIB version 1.10.0 Index]